Giovanni Palla

I think imports are still wrong, see error ``` n:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin [2819] /home/runner/work/squidpy/squidpy$ /home/runner/work/squidpy/squidpy/.tox/py310-linux/bin/python -m pytest --cov --cov-append --cov-report=term-missing --cov-config=/home/runner/work/squidpy/squidpy/tox.ini --ignore docs/ -vv --test-napari ImportError while loading conftest '/home/runner/work/squidpy/squidpy/tests/conftest.py'. tests/conftest.py:23: in...

> @giovp I did apply the changes, there were some minor things i had to change though. It's on the spatialde repo. what type of changes?

close #599

will close this following this conversation https://github.com/scverse/scanpy/pull/2296#issuecomment-1273309536

hi @ruqianl , I'd suggest to use the squidpy functions https://squidpy.readthedocs.io/en/latest/examples.html#plotting and for vizgen, pass `shape=None` hth

hi @ruqianl did you manage to solve the issue?

hi @sophieRAIBAUD , thanks for the issue, I think the only way is by doing it manual. I think loupe actually provides a way to correct/subset the spots under tissue,...

hi @sophieRAIBAUD , > Is it possible to annotate the data with something else than TRUE or FALSE ? for example, how can I create this annotation: unfortunately no, but...

mmh this is really weird, are you sure you passed the same anndata to napari construction and the on you get for the index?

but it shoiuldn't be. I think you can return the obs_names from the boolean obs and then use those to subset the original anndata you'd want to subset? Sorry, it...